Acute kidney injury (AKI) is a common clinical syndrome and an independent risk factor of chronic kidney disease and end-stage renal failure. At present, the treatments of AKI are still very limited and the morbidity and mortality of AKI are rising.
Non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs and circular RNAs (circRNAs), are RNAs that are transcribed from the genome, but not translated into proteins.
It has been widely reported that ncRNA is involved in AKI caused by ischemia reperfusion injury (IRI), drugs and sepsis through different molecular biological mechanisms, such as apoptosis and oxidative stress response. Therefore, ncRNAs are expected to become a new target for clinical prevention and treatment of AKI and a new biomarker for early warning of the occurrence and prognosis of AKI.
Here, the role and mechanism of ncRNA in AKI and the research progress of ncRNA as biomarkers are reviewed.
Effect of imputation on gene network reconstruction from single-cell RNA-seq data.
Despite the advances in single-cell transcriptomics, the reconstruction of gene regulatory networks remains challenging.
Both the large amount of zero counts in experimental data and the lack of a consensus preprocessing pipeline for single-cell RNA sequencing (scRNA-seq) data make it hard to infer networks.
Imputation can be applied in order to enhance gene-gene correlations and facilitate downstream analysis.
However, it is unclear what consequences imputation methods have on the reconstruction of gene regulatory networks.
To study this, we evaluate the differences on the performance and structure of reconstructed networks before and after imputation in single-cell data.
We observe an inflation of gene-gene correlations that affects the predicted network structures and may decrease the performance of network reconstruction in general.
However, within the modest limits of achievable results, we also make a recommendation as to an advisable combination of algorithms while warning against the indiscriminate use of imputation before network reconstruction in general.
However, within the modest limits of achievable results, we also make a recommendation as to an advisable combination of algorithms while warning against the indiscriminate use of imputation before network reconstruction in general.
POIBM: Batch correction of heterogeneous RNA-seq datasets through latent sample matching.
- RNA sequencing and other high-throughput technologies are essential in understanding complex diseases, such as cancers, but are susceptible to technical factors manifesting as patterns in the measurements. These batch patterns hinder the discovery of biologically relevant patterns. Unbiased batch effect correction in heterogeneous populations currently requires special experimental designs or phenotypic labels, which are not readily available for patient samples in existing datasets.
- We present POIBM, an RNA-seq batch correction method, which learns virtual reference samples directly from the data. We use a breast cancer cell line dataset to show that POIBM exceeds or matches the performance of previous methods, while being blind to the phenotypes. Further, we analyze The Cancer Genome Atlas RNA-seq data to show that batch effects plague many cancer types; POIBM effectively discovers the true replicates in stomach adenocarcinoma; and integrating the corrected data in endometrial carcinoma improves cancer subtypin.
Circular RNA circ_0001459 accelerates hepatocellular carcinoma progression via the miR-6165/IGF1R axis.
- An increasing amount of evidence shows that circular RNAs (circRNAs) have critical effects on cancer progression and development; however, the biological function and potential molecular mechanism of circRNAs in hepatocellular carcinoma (HCC) are still unclear.
- CircRNA sequencing was used to identify differentially expressed circRNAs between HCC tissue and adjacent normal tissue. We found that circ_0001459 expression was significantly elevated in HCC tissue and cell lines.
- Furthermore, in vitro and in vivo functional experiments were carried out to detect the effects of circ_0001459 on HCC growth and metastasis.
- Knockdown of circ_0001459 significantly inhibited the proliferation, migration, and invasion of HCC cells, whereas upregulation of circ_0001459 had the opposite effect.
- Moreover, bioinformatics analysis, dual-luciferase reporter assay, RNA immunoprecipitation, and fluorescence in situ hybridization assays were used to predict and verify the interaction between circ_0001459, miR-6165, and the target gene IGF1R.
- Downregulation of circ_0001459 decreased IGF1R expression and inhibited epithelial-to-mesenchymal transition, which could be rescued by treatment with a miR-6165 inhibitor.
- Mechanistically, we revealed that circ_0001459 could sponge miR-6165 and induce the upregulation of its downstream target IGF1R, thus significantly promoting the progression of HCC. Therefore, circ_0001459 could be a new potential therapeutic target for HCC patients.
Cryo-EM advances in RNA structure determination.
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution.
Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo-EM because measurements are carried out under near-native crystal-free conditions, and large protein complexes with conformational and compositional heterogeneity are readily resolved.
RNA has remained underexplored in cryo-EM, despite its essential role in various biological processes.
This review highlights current challenges and recent progress in using cryo-EM single-particle analysis to determine protein-free RNA structures, enabled by improvement in sample preparation and integration of multiple structural and biochemical methods.
Circular RNA as a Potential Biomarker for Forensic Age Prediction.
- In forensic science, accurate estimation of the age of a victim or suspect can facilitate the investigators to narrow a search and aid in solving a crime. Aging is a complex process associated with various molecular regulations on DNA or RNA levels.
- Recent studies have shown that circular RNAs (circRNAs) upregulate globally during aging in multiple organisms such as mice and C.elegans because of their ability to resist degradation by exoribonucleases. In the current study, we attempted to investigate circRNAs’ potential capability of age prediction.
- Here, we identified more than 40,000 circRNAs in the blood of thirteen Chinese unrelated healthy individuals with ages of 20-62 years according to their circRNA-seq profiles.
- Three methods were applied to select age-related circRNA candidates including the false discovery rate, lasso regression, and support vector machine.
- The analysis uncovered a strong bias for circRNA upregulation during aging in human blood. A total of 28 circRNAs were chosen for further validation in 30 healthy unrelated subjects by RT-qPCR, and finally, 5 age-related circRNAs were chosen for final age prediction models using 100 samples of 19-73 years old.
- Several different algorithms including multivariate linear regression (MLR), regression tree, bagging regression, random forest regression (RFR), and support vector regression (SVR) were compared based on root mean square error (RMSE) and mean average error (MAE) values.
- Among five modeling methods, regression tree and RFR performed better than the others with MAE values of 8.767 years (S.rho = 0.6983) and 9.126 years (S.rho = 0.660), respectively.
- Sex effect analysis showed age prediction models significantly yielded smaller prediction MAE values for males than females (MAE = 6.133 years for males, while 10.923 years for females in the regression tree model).
Multi‐Level, 10 ampuls each level (Levels 1, 2, 3) |
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| CC527 | RNA Medical | each | 169 EUR |
Level 1, 30 ampuls |
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| CC527-1 | RNA Medical | each | 169 EUR |
Level 2, 30 ampuls |
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| CC527-2 | RNA Medical | each | 169 EUR |
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| CC527-3 | RNA Medical | each | 169 EUR |
ESA LEADCARE II ANALYZER KIT |
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ESA LEADCARE II TEST KIT |
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Safe-Wrap® Combo Blood Collection Tubes for i•-STAT® (Package of 50 Tubes) 95μL |
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| CT095 | RNA Medical | each | 85 EUR |
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| CT220 | RNA Medical | each | 191 EUR |
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Multi‐Level, 10 ampuls each level (Levels 1, 2, 3) |
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Level 1, 30 ampuls |
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| QC253-1 | RNA Medical | each | 221 EUR |
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| QC253-2 | RNA Medical | each | 221 EUR |
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| QC253-3 | RNA Medical | each | 221 EUR |
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In the current study, we first used circRNAs as additional novel age-related biomarkers for developing forensic age estimation models.
We propose that the use of circRNAs to obtain additional clues for forensic investigations and serve as aging indicators for age prediction would become a promising field of interest.